HEADER IMMUNE SYSTEM 14-MAY-20 6Z1Z TITLE STRUCTURE OF THE ANTI-CD9 NANOBODY 4C8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NANOBODY 4C8; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_COMMON: LLAMA; SOURCE 4 ORGANISM_TAXID: 9844; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: CODON PLUS (RIL); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PHEN6 KEYWDS NANOBODY, CD9-BINDING, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR N.NEVIANI,W.OOSTERHEERT,N.M.PEARCE,M.LUTZ,L.M.J.KROON-BATENBURG, AUTHOR 2 P.GROS REVDAT 4 09-OCT-24 6Z1Z 1 REMARK REVDAT 3 24-JAN-24 6Z1Z 1 REMARK REVDAT 2 30-SEP-20 6Z1Z 1 JRNL REVDAT 1 23-SEP-20 6Z1Z 0 JRNL AUTH W.OOSTERHEERT,K.T.XENAKI,V.NEVIANI,W.POS,S.DOULKERIDOU, JRNL AUTH 2 J.MANSHANDE,N.M.PEARCE,L.M.KROON-BATENBURG,M.LUTZ, JRNL AUTH 3 P.M.VAN BERGEN EN HENEGOUWEN,P.GROS JRNL TITL IMPLICATIONS FOR TETRASPANIN-ENRICHED MICRODOMAIN ASSEMBLY JRNL TITL 2 BASED ON STRUCTURES OF CD9 WITH EWI-F. JRNL REF LIFE SCI ALLIANCE V. 3 2020 JRNL REFN ESSN 2575-1077 JRNL PMID 32958604 JRNL DOI 10.26508/LSA.202000883 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 23713 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM 5% OF DATA REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1170 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.78 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2787 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.29 REMARK 3 BIN R VALUE (WORKING SET) : 0.3234 REMARK 3 BIN FREE R VALUE SET COUNT : 145 REMARK 3 BIN FREE R VALUE : 0.3015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1772 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.229 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : NULL NULL NULL NULL REMARK 3 ORIGIN FOR THE GROUP (A): 12.0108 -2.3112 0.9649 REMARK 3 T TENSOR REMARK 3 T11: 0.1185 T22: 0.1428 REMARK 3 T33: 0.1395 T12: -0.0003 REMARK 3 T13: -0.0076 T23: -0.0181 REMARK 3 L TENSOR REMARK 3 L11: 1.5963 L22: 1.2392 REMARK 3 L33: 1.4819 L12: -0.4848 REMARK 3 L13: -0.0202 L23: -0.0587 REMARK 3 S TENSOR REMARK 3 S11: 0.0459 S12: 0.1163 S13: -0.0739 REMARK 3 S21: -0.1543 S22: -0.1029 S23: -0.0346 REMARK 3 S31: -0.0133 S32: -0.0850 S33: -0.0237 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : NULL NULL NULL NULL REMARK 3 ORIGIN FOR THE GROUP (A): 12.1110 10.8401 -26.7783 REMARK 3 T TENSOR REMARK 3 T11: 0.1349 T22: 0.1453 REMARK 3 T33: 0.1493 T12: 0.0040 REMARK 3 T13: -0.0090 T23: -0.0171 REMARK 3 L TENSOR REMARK 3 L11: 1.7406 L22: 0.7169 REMARK 3 L33: 2.3527 L12: 0.2903 REMARK 3 L13: -0.5463 L23: -0.0504 REMARK 3 S TENSOR REMARK 3 S11: 0.0524 S12: -0.1346 S13: 0.1300 REMARK 3 S21: 0.0857 S22: -0.0730 S23: 0.0699 REMARK 3 S31: -0.0192 S32: 0.0393 S33: 0.0084 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.11 REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6Z1Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1292108739. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8731 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 X 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : EVAL15 REMARK 200 DATA SCALING SOFTWARE : EVAL15 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23719 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 24.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.12900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 1.05700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5IMK REMARK 200 REMARK 200 REMARK: NEEDLE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 20% (W/V) PEG REMARK 280 8,000 THE CRYSTAL WAS CRYOPROTECTED BY SOAKING IN RESERVOIR REMARK 280 SOLUTION SUPPLEMENTED WITH 30% (V/V) PEG 400, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 20.70850 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 103 REMARK 465 THR A 104 REMARK 465 GLY A 105 REMARK 465 HIS A 122 REMARK 465 GLY A 123 REMARK 465 SER A 124 REMARK 465 GLY A 125 REMARK 465 LEU A 126 REMARK 465 VAL A 127 REMARK 465 PRO A 128 REMARK 465 ARG A 129 REMARK 465 GLY B 103 REMARK 465 THR B 104 REMARK 465 GLY B 105 REMARK 465 HIS B 122 REMARK 465 GLY B 123 REMARK 465 SER B 124 REMARK 465 GLY B 125 REMARK 465 LEU B 126 REMARK 465 VAL B 127 REMARK 465 PRO B 128 REMARK 465 ARG B 129 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 1 CG CD OE1 OE2 REMARK 470 ARG A 27 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 43 CG CD CE NZ REMARK 470 LYS A 76 CG CD CE NZ REMARK 470 ARG A 101 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 107 CG CD CE NZ REMARK 470 GLU B 1 CG CD OE1 OE2 REMARK 470 GLN B 3 CG CD OE1 NE2 REMARK 470 GLN B 13 CG CD OE1 NE2 REMARK 470 ARG B 27 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 43 CG CD CE NZ REMARK 470 GLU B 44 CG CD OE1 OE2 REMARK 470 LYS B 76 CG CD CE NZ REMARK 470 ARG B 101 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 107 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER B 25 -63.63 -120.33 REMARK 500 ARG B 27 157.54 -46.76 REMARK 500 LYS B 43 157.68 -47.29 REMARK 500 ALA B 92 168.51 177.41 REMARK 500 ARG B 101 -152.80 -124.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6RLR RELATED DB: PDB REMARK 900 STRUCTURE OF THE EC2 DOMAIN OF CD9 WITHOUT NANOBODY BOUND, THIS REMARK 900 STRUCTURE WAS UPLOADED TO THE PDB PREVIOUSLY REMARK 900 RELATED ID: 6Z1V RELATED DB: PDB REMARK 900 STRUCTURE OF THE EC2 DOMAIN OF CD9 IN COMPLEX WITH NANOBODY 4E8 DBREF 6Z1Z A 1 129 PDB 6Z1Z 6Z1Z 1 129 DBREF 6Z1Z B 1 129 PDB 6Z1Z 6Z1Z 1 129 SEQRES 1 A 129 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 129 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 A 129 ARG THR PHE SER ASP TYR VAL MET GLY TRP PHE ARG GLN SEQRES 4 A 129 ALA PRO GLY LYS GLU ARG THR PHE VAL ALA ARG ILE GLY SEQRES 5 A 129 TRP SER GLY ASP LEU THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 A 129 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 A 129 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 A 129 ALA ILE TYR TYR CYS ALA ALA ASP GLU ARG TRP GLY THR SEQRES 9 A 129 GLY GLY LYS PHE ASP TYR TRP GLY GLN GLY THR GLN VAL SEQRES 10 A 129 THR VAL SER SER HIS GLY SER GLY LEU VAL PRO ARG SEQRES 1 B 129 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 129 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 B 129 ARG THR PHE SER ASP TYR VAL MET GLY TRP PHE ARG GLN SEQRES 4 B 129 ALA PRO GLY LYS GLU ARG THR PHE VAL ALA ARG ILE GLY SEQRES 5 B 129 TRP SER GLY ASP LEU THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 B 129 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 B 129 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 B 129 ALA ILE TYR TYR CYS ALA ALA ASP GLU ARG TRP GLY THR SEQRES 9 B 129 GLY GLY LYS PHE ASP TYR TRP GLY GLN GLY THR GLN VAL SEQRES 10 B 129 THR VAL SER SER HIS GLY SER GLY LEU VAL PRO ARG FORMUL 3 HOH *140(H2 O) HELIX 1 AA1 THR A 28 TYR A 32 5 5 HELIX 2 AA2 LYS A 87 THR A 91 5 5 HELIX 3 AA3 THR B 28 TYR B 32 5 5 HELIX 4 AA4 ASN B 74 LYS B 76 5 3 HELIX 5 AA5 LYS B 87 THR B 91 5 5 SHEET 1 AA1 4 GLN A 3 SER A 7 0 SHEET 2 AA1 4 LEU A 18 SER A 25 -1 O SER A 21 N SER A 7 SHEET 3 AA1 4 THR A 78 MET A 83 -1 O MET A 83 N LEU A 18 SHEET 4 AA1 4 PHE A 68 ASP A 73 -1 N SER A 71 O TYR A 80 SHEET 1 AA2 6 GLY A 10 GLN A 13 0 SHEET 2 AA2 6 THR A 115 SER A 120 1 O THR A 118 N VAL A 12 SHEET 3 AA2 6 ALA A 92 ASP A 99 -1 N TYR A 94 O THR A 115 SHEET 4 AA2 6 VAL A 33 GLN A 39 -1 N VAL A 33 O ASP A 99 SHEET 5 AA2 6 THR A 46 ILE A 51 -1 O THR A 46 N ARG A 38 SHEET 6 AA2 6 THR A 58 TYR A 60 -1 O TYR A 59 N ARG A 50 SHEET 1 AA3 4 GLY A 10 GLN A 13 0 SHEET 2 AA3 4 THR A 115 SER A 120 1 O THR A 118 N VAL A 12 SHEET 3 AA3 4 ALA A 92 ASP A 99 -1 N TYR A 94 O THR A 115 SHEET 4 AA3 4 TYR A 110 TRP A 111 -1 O TYR A 110 N ALA A 98 SHEET 1 AA4 4 LEU B 4 SER B 7 0 SHEET 2 AA4 4 LEU B 18 ALA B 24 -1 O SER B 21 N SER B 7 SHEET 3 AA4 4 THR B 78 MET B 83 -1 O MET B 83 N LEU B 18 SHEET 4 AA4 4 PHE B 68 ASP B 73 -1 N SER B 71 O TYR B 80 SHEET 1 AA5 6 GLY B 10 GLN B 13 0 SHEET 2 AA5 6 THR B 115 SER B 120 1 O SER B 120 N VAL B 12 SHEET 3 AA5 6 ALA B 92 ASP B 99 -1 N TYR B 94 O THR B 115 SHEET 4 AA5 6 VAL B 33 GLN B 39 -1 N VAL B 33 O ASP B 99 SHEET 5 AA5 6 ARG B 45 ILE B 51 -1 O ALA B 49 N TRP B 36 SHEET 6 AA5 6 THR B 58 TYR B 60 -1 O TYR B 59 N ARG B 50 SHEET 1 AA6 4 GLY B 10 GLN B 13 0 SHEET 2 AA6 4 THR B 115 SER B 120 1 O SER B 120 N VAL B 12 SHEET 3 AA6 4 ALA B 92 ASP B 99 -1 N TYR B 94 O THR B 115 SHEET 4 AA6 4 TYR B 110 TRP B 111 -1 O TYR B 110 N ALA B 98 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.03 SSBOND 2 CYS B 22 CYS B 96 1555 1555 2.03 CRYST1 48.901 41.417 56.853 90.00 89.69 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.020449 0.000000 -0.000110 0.00000 SCALE2 0.000000 0.024145 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017589 0.00000